Origin of symmetrical triradial chromosomes in human cells

We have collected 23 sporadic symmetrical triradial chromosomes (plus one D with duplicate satellites), 22 from cultured lymphocytes and one from a bone marrow cell. Fifteen triradials were from patients with Bloom's syndrome, and two from a Fanconi's anemia patient. The following chromosomes and chromosome groups were involved: 1, 2, 3, 4, 5, C (11 identified), D, and 17. The branchpoints were localized nonrandomly. Regions in or near centric heterochromatin were often involved. Some of the branchpoints are regions which also contain a high number of mitotic chiasmata. When the present sporadic triradials combined with those from the literature were compared with triradials with branchpoints in the fragile regions, the localized branchpoints were different in these two groups. Our conclusion that most — possibly all — symmetrical triradials are caused by partial endoreduplication is based on the following observations: the shape of the triradials which shows that the extra segments are paired with their intact sister chromatids and not with each other; the failure of X-rays in G₂ to increase the incidence of symmetrical triradials; the fact that in some cases the end of the extra segment is joined to its intact sister chromatid; and the occurrence of duplicate satellites.     

Models for the evolution of protandry in insects

Protandry is the tendency for males to emerge before females, and it is common in insects with discrete, nonoverlapping generations in which females mate once only soon after emergence. In these circumstances males which emerge early will have more opportunities to mate than those which emerge late, so that protandry would be expected to evolve through sexual selection. In diploid species in which the primary sex ratio is fixed, protandry can evolve only through shortening the developmental time of males, so changing the distribution of their emergence times. Two models of the evolution of protandry in this way are compared. The first model assumes that the distribution of male emergence times can respond without any constraint to sexual selection, so leading to an “ideal free” distribution; the second model assumes that the distribution can shift only in mean (or possibly in mean and variance), but not in shape.     

Quantifying neuronal size: summing up trees and splitting the branch difference

Neurons vary greatly in size, shape, and complexity depending on their underlying function. Overall size of neuronal trees affects connectivity, area of influence, and other biophysical properties. Relative distributions of neuronal extent, such as the difference between subtrees at branch points, are also critically related to function and activity. This review covers neuromorphological research that analyzes shape and size to elucidate their functional role for different neuron types. We also introduce a novel morphometric, “caulescence”, capturing the extent to which trees exhibit a main path. Neuronal tree types differ vastly in caulescence, suggesting potential neurocomputational correlates of this property.     

On the role of patch density and patch variability in central-place foraging

Existing models of the foraging behavior of single-prey loaders in patchy environments differ on whether the optimal forager is predicted to stay in a patch until a prey is found, or to leave a patch for a next one if a prey is not found by a certain “deadline.” This article examines conditions on the probability distribution of prey density across patches that are necessary or sufficient for the existence of a finite, optimal deadline. It is shown that, for environments in which prey density is variable but never falls below some strictly positive level, a finite, optimal deadline exists when and only when the spatial density of patches is “high.” Also, a characterization is given of a large class of distributions (including the gamma distribution) for which a finite, optimal deadline exists for all levels of spatial density of patches.     

Centrifugal-order distributions in binary topological trees

Statistical properties of topological binary trees are studied on the basis of the distribution of segments in relation to centrifugal order. Special attention is paid to the mean of this distribution in a tree as it will be used as a measure of tree topology. It will be shown how the expectation of the mean centrifugal order depends both on the size of the tree and on the mode of growth in the context of modelling the growth of tree structures. Observed trees can be characterized by their mean orders and procedures are described to find the growth mode that optimally corresponds to these data. The variance structure of the mean-order measure appears to be a crucial factor in these fitting procedures. Examples indicate that mean-order analysis is an accurate alternative to partition analysis that is based on the partitioning of segments over sub-tree pairs at branching points.     

The use of precision dendrometers in research on daily stem size and wood property variation: A review

Dendrometers are instruments which are used to measure the diameters of trees. This review considers the use of dendrometers with high spatial and temporal precision in past and present research, the value of which is increasingly being realised. Various insights into tree growth and physiology can be obtained using high-resolution dendrometers, including the assessment of stem daily water status and the understanding of short-term growth responses to changing environmental conditions. This kind of data is useful for irrigation scheduling, assessing site quality, and developing models of the main drivers of tree growth at sub-diurnal resolution. A third, more novel application is the potential these instruments provide as a “template” that relates temporal measurement of growth to spatial measurements of wood properties. Accordingly, this kind of “re-scaled” data is useful in linking environmental conditions which prevailed as the wood formed to varying wood properties along a pith-to-bark wood profile of the sort generated by systems like CSIRO's SilviScan™. This can provide valuable insights into how tree ring structure and radially varying wood properties represent past climates. The development of dendrometers, their use in these three main areas, and a systematic approach to growth-wood property rescaling is discussed in this review.     

Some nonstandard modeling techniques in theoretical biology

Three topics are surveyed. (1) The quasisteady-state assumption is a fundamental example of frequent instances in theoretical biology where advantage can be taken of the simultaneous existence of widely separated time scales. It is shown that appropriate scaling can provide a markedly sharper estimate of the range of validity of this approximation. (2) A new methodology for modelling dynamically changing networks is applied to simple morphogenesis in fungal colonies. A brief discussion is given of possible application to the complex polymerization and cross-linking that characterize cytoplasmic fibers. (3) It is shown that problems in ecology and immunology can be illuminated by considering nonlocal interactions (and hence integrodifferential equations) that generate patterns in “aspect space” or “shape space.”     

Morphological and molecular investigations of Paramecium schewiakoffi sp. nov. (Ciliophora, Oligohymenophorea) and current status of distribution and taxonomy of Paramecium spp.

Paramecium schewiakoffi sp. nov. is described from a pond in Shanghai, China. It is a freshwater species belonging to the “aurelia” subgroup of the genus. It is of similar size and shape to P. jenningsi, but has a single large micronucleus of the “chromosomal” morphological type, while P. jenningsi has two smaller micronuclei. The general morphology, morphometric characteristics and nuclear reorganization pattern, a random amplified polymorphic DNA (RAPD) fingerprint pattern, and the small subunit rRNA gene sequence are presented for the species. Comparison of P. schewiakoffi with the other species of Paramecium indicates that it is a valid new species of the genus. Geographical locations reported for many Paramecium species do not support the theory that all ciliates have a cosmopolitan distribution. It is proposed that, in an extension of Jankowski's earlier suggestion, the genus Paramecium should be subdivided into four subgenera: Chloroparamecium, Helianter, Cypriostomum and Paramecium, on the basis of morphometric, biological and molecular differences.     

Competition-dependent modelling of foliage biomass in forest stands

Currently, foliage biomass is estimated based on stem diameter or basal area. However, it is questionable whether the relations between foliage and stem observed from plantations of a single tree species can be applied to stands of different structure or species composition. In this paper, a procedure is presented to simulate foliage and branch biomass of tree crowns relative to crown size and light competition. Crowns are divided into layers and segments and each segment is divided into a foliated and an unfoliated fraction. Depending on the competitive status of the segment, leaf area density, specific leaf area and foliated branch fraction are determined. Based on this information, foliage biomass is calculated. The procedure requires a crown shape function and a measure to characterise competition for light and space of each individual segment within the canopy. Simple solutions are suggested for both requirements to enable an application with data that can be measured non-destructively in the field; these were stem position, tree height, crown base height, crown radii and some general crown shape information. The model was parameterised from single trees of Norway spruce and European beech and partly evaluated with independent data close to the investigation plot. Evaluations showed that the model can attribute the ecology of the different crown forms. Modelled foliage distribution for beech and spruce as well as total needle biomass of spruce agreed well with measurements but foliage biomass of beech was underestimated. The results are discussed in the context of a general model application in structured forests.     

Heterogeneous perfusion is a consequence of uniform shear stress in optimized arterial tree models

Using optimized computer models of arterial trees we demonstrate that flow heterogeneity is a necessary consequence of a uniform shear stress distribution. Model trees are generated and optimized under different modes of boundary conditions. In one mode flow is delivered to the tissue as homogeneously as possible. Although this primary goal can be achieved, resulting shear stresses between blood and the vessel walls show very large spread. In a second mode, models are optimized under the condition of uniform shear stress in all segments which in turn renders flow distribution heterogeneous. Both homogeneous perfusion and uniform shear stress are desirable goals in real arterial trees but each of these goals can only be approached at the expense of the other. While the present paper refers only to optimized models, we assume that this dual relation between the heterogeneities in flow and shear stress may represent a more general principle of vascular systems.     

A basic limitation on inferring phylogenies by pairwise sequence comparisons

Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences, and from them construct a value that, in expectation, is additive under a stochastic model of site substitution. Most models assume a distribution of rates across sites, often based on a gamma distribution. Provided the (shape) parameter of this distribution is known, the method can correctly reconstruct the tree. However, if the shape parameter is not known then we show that topologically different trees, with different shape parameters and associated positive branch lengths, can lead to exactly matching distributions on pairwise site patterns between all pairs of taxa. Thus, one could not distinguish between the two trees using pairs of sequences without some prior knowledge of the shape parameter. More surprisingly, this can happen for any choice of distinct shape parameters on the two trees, and thus the result is not peculiar to a particular or contrived selection of the shape parameters. On a positive note, we point out known conditions where identifiability can be restored (namely, when the branch lengths are clocklike, or if methods such as maximum likelihood are used).     

Unmanned Aerial Survey of Fallen Trees in a Deciduous Broadleaved Forest in Eastern Japan

Since fallen trees are a key factor in biodiversity and biogeochemical cycling, information about their spatial distribution is of use in determining species distribution and nutrient and carbon cycling in forest ecosystems. Ground-based surveys are both time consuming and labour intensive. Remote-sensing technology can reduce these costs. Here, we used high-spatial-resolution aerial photographs (0.5–1.0 cm per pixel) taken from an unmanned aerial vehicle (UAV) to survey fallen trees in a deciduous broadleaved forest in eastern Japan. In nine sub-plots we found a total of 44 fallen trees by ground survey. From the aerial photographs, we identified 80% to 90% of fallen trees that were >30 cm in diameter or >10 m in length, but missed many that were narrower or shorter. This failure may be due to the similarity of fallen trees to trunks and branches of standing trees or masking by standing trees. Views of the same point from different angles may improve the detection rate because they would provide more opportunity to detect fallen trees hidden by standing trees. Our results suggest that UAV surveys will make it possible to monitor the spatial and temporal variations in forest structure and function at lower cost.     

藏东南川滇高山栎种群不同生长阶段的空间格局与关联性

运用点格局分析方法中Ripley L函数,对藏东南川滇高山栎种群不同生长阶段的空间格局及其关联性进行分析.结果表明： 藏东南川滇高山栎种群径级结构呈单峰型,小树与中树的数量在整个种群中占绝对优势,整个种群自然更新状况良好,属增长型种群.川滇高山栎种群在从小树发育到大树的过程中,小树、中树在小尺度上均呈明显的聚集分布,而大树在整个尺度上基本上呈随机分布.小树与中树、大树间在小尺度上有显著的相关性,而中树与大树不相关.川滇高山栎种群在从小树、中树发育到大树的过程中,其空间格局由聚集分布到随机分布.川滇高山栎种群的自然更新受种间竞争的影响,也受种内竞争的影响.在自然环境条件相似下,影响川滇高山栎种群分布格局的最主要因素是其自身的生物、生态学特性.     

Kinetoplast DNA in the insect trypanosomes Crithidia luciliae and Crithidia fasciculata: III. Heteroduplex analysis of the C. luciliae minicircles

We have investigated the nature of the sequence heterogeneity of the minicircles of Crithidia luciliae kinetoplast DNA by EM heteroduplex analysis of minicircles cleaved with endonuclease HindIII. Approximately 40% of the minicircles showed—after denaturation and reannealing—structures indicative of sequence rearrangements: the majority contained heteroduplex “eyes” interpreted as due to inversions; about 10% of the heteroduplexes yielded structures interpreted as due to translocations and a similar fraction showed insertions and deletions. The category of “eyed” molecules was analyzed in detail: four minicircle segments were found that displayed a high incidence of such eyes indicating that the rearrangements were not scattered at random over the minicircles. Moreover, since also “eyes” were found overlapping two or three of the four regions, we postulate that these segments are capable of recombining with each other. We conclude that specific segmental rearrangements form the main basis of the minicircle sequence heterogeneity in Crithidia.     

The stochastic community and the logistic-J distribution

A new formal model called the multispecies logistical (MSL) system produces species/abundance distributions that are compared statistically with those found in natural communities. The system, which is able to handle thousands of individuals from hundreds of species, iteratively selects random pairs of individuals and transfers a unit of biomass (or energy) between the respective species. Several elaborations of the model, including those with trophic compartments, appear to produce the same distribution. The theoretical distribution underlying the MSL system is a hyperbolic section, here called the logistic-J distribution. In the study reported here, the logistic-J distribution has been fitted to the species-abundance histograms of 125 randomly selected taxocoenoses. Since the overall chi square score of the logistic-J achieved near-optimality in this study, it cannot be distinguished statistically from the J-curves observed by field biologists. For comparison, the log-series distribution was given the same test and scored significantly higher (more poorly) than the mean logistic-J score. If there is a single, major distribution underlying natural communities, it is not the log-series distribution. Nor, owing to a mathematical error in its formulation, can it be the lognormal distribution. In the MSL system each species follows a “stochastic orbit” about the mean abundance producing, in consequence, the logistic-J distribution. Such orbits are produced by any system in which the probabilities of reproduction and death are approximately equal. Accordingly, the “stochastic communities hypothesis” is proposed here as the overall mechanism governing abundances in all natural communities. It is not a single mechanism, per se, but the net effect of all environmental influences.     

Visual shape recognition with contour propagation

A neural architecture is presented that encodes the visual space inside and outside of a shape. The contours of a shape are propagated across an excitable neuronal map and fed through a set of orientation columns, thus creating a pattern which can be viewed as a vector field. This vector field is then burned as synaptic, directional connections into a propagation map, which will serve as a “shape map”. The shape map identifies its own, preferred input when it is translated, deformed, scaled and fragmented, and discriminates other shapes very distinctively. Encoding visual space is much more efficient for shape recognition than determining contour geometry only.     

Crystalline inclusions in hepatocytes and associated interhepatocytic macrophages from female Ohrid trout (Salmo letnica Kar.)

When characterizing the liver ultrastructure in Ohrid trout, we noticed that cells often displayed unusual cytoplasmic crystalline inclusions. Their morphology varied much, concerning the size, shape and electron density, showing aspects never reported in fish liver. In hepatocytes, the inclusions existed in close topographical relationship with dense bodies (often within them). Such “crystals” inclusions also existed in macrophages and in biliary passages lumina. Data revealed seasonal/breeding-related changes of the dense bodies and crystalline inclusions within hepatocytes; decreasing from the earliest to the more advanced ovary maturation stages. Additionally, based on the negative correlations between the amounts of dense bodies and of “crystals” and the ovary somatic ratio, we suggested there might be connections between the sex steroids status and the inclusions formation. A positive correlation between the quantities of “crystals” and of dense bodies further suggested that the inclusions might derive from normal processes, e.g., the females’ cyclic liver changes, that involves dense bodies’ turnover. However, a toxicological aetiology cannot be excluded. Additionally, multiple mechanisms can contribute to the “crystals” genesis. Facing literature reports and because the inclusions content seemed washed out during tissue processing, they are likely lipid in nature, but their exact composition and genesis require further analyses.     

Resource availability and disturbance shape maximum tree height across the Amazon

Tall trees are key drivers of ecosystem processes in tropical forest, but the controls on the distribution of the very tallest trees remain poorly understood. The recent discovery of grove of giant trees over 80 meters tall in the Amazon forest requires a reevaluation of current thinking. We used high‐resolution airborne laser surveys to measure canopy height across 282,750 ha of old‐growth and second‐growth forests randomly sampling the entire Brazilian Amazon. We investigated how resources and disturbances shape the maximum height distribution across the Brazilian Amazon through the relations between the occurrence of giant trees and environmental factors. Common drivers of height development are fundamentally different from those influencing the occurrence of giant trees. We found that changes in wind and light availability drive giant tree distribution as much as precipitation and temperature, together shaping the forest structure of the Brazilian Amazon. The location of giant trees should be carefully considered by policymakers when identifying important hot spots for the conservation of biodiversity in the Amazon.     

FMRFamide tagging—how an ionotropic receptor can be used to measure peptide secretion

In this chapter, we describe a technique, FMRFamide tagging, that in principle can be used to measure the release of any sequenced neuropeptide. The method relies upon the addition of an “electrophysiologically active” tag to the prohormone that encodes the neuropeptide of interest. Secretion of the electrophysiological tag (and thus the peptide of interest) is detected by activation of the ionotropic “tag receptor.” Both the tagged prohormone and the tag receptor are expressed in the cell type under investigation. Since the tag and the neuropeptide of interest are on the same prohormone they are co-secreted and thus secretion of the tag reflects the co-secretion of the neuropeptide of interest. This method can be used to detect neuropeptide secretion on a millisecond timescale.     

The mechanical significance of the occlusal geometry of great ape molars in food breakdown

Analyses of dental function are an essential component of the study of human evolution. However, with few exceptions, they have utilized the traditional analogizing method of comparative anatomy, and have assumed rather than demonstrated that proposed adaptive characters confer a performance benefit. Since food reduction is a mechanical process, it is appropriate to measure performance using mechanical parameters, specifically the ability of a given morphology to induce failure in food particle by either of the two major regimes: crush and shear, corresponding to simple stresses (tensile and compressive) and shear stress, respectively. We apply finite elements stress analysis to model the relationship between the angulation of the intercuspal occlusal surfaces in a “puncture crushing” mode of mastication. On the basis of morphological data acquired from sectioned great ape molars, we have predicted the nature, magnitude and distribution of stress in a standard food particle by models representing each morphotype. Results indicate that the blunt-cusped molars ofHomo, the gradually-sloping supporting (buccal) cusps but high-angled guiding (lingual) cusps of the lower molars ofPan, and the high angled occlusal surfaces ofGorillaare all more likely to fracture small food particles by shear, while the gradually sloping occlusal surfaces ofPongomolars are more likely to break them down by “crush”. Mechanisms of food failure induced by molars ofPanandHomowill vary according to the orientation of the tooth–food contacting surfaces, which in turn will vary according to the size of the food particle. These genera may be able to break food down either by shear or by “crush”.